Tcf15 (transcription factor 15) - Rat Genome Database

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Gene: Tcf15 (transcription factor 15) Rattus norvegicus
Analyze
Symbol: Tcf15
Name: transcription factor 15
RGD ID: 1308464
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; E-box binding activity; and bHLH transcription factor binding activity. Predicted to contribute to DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II; regulation of stem cell differentiation; and stem cell population maintenance. Predicted to act upstream of or within several processes, including epithelial cell differentiation; paraxial mesoderm development; and post-anal tail morphogenesis. Predicted to be located in nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Orthologous to human TCF15 (transcription factor 15); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC296272
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23140,638,984 - 140,644,766 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,638,984 - 140,644,766 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3144,543,478 - 144,549,262 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03153,127,302 - 153,133,086 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03150,867,901 - 150,873,677 (+)NCBIRnor_WKY
Rnor_6.03147,643,250 - 147,649,511 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,643,250 - 147,649,504 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03153,992,077 - 153,998,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,491,664 - 142,497,446 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13142,397,247 - 142,402,918 (+)NCBI
Celera3139,391,601 - 139,397,369 (+)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7588439   PMID:8955271   PMID:18361414   PMID:24038871  


Genomics

Comparative Map Data
Tcf15
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23140,638,984 - 140,644,766 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,638,984 - 140,644,766 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3144,543,478 - 144,549,262 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03153,127,302 - 153,133,086 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03150,867,901 - 150,873,677 (+)NCBIRnor_WKY
Rnor_6.03147,643,250 - 147,649,511 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,643,250 - 147,649,504 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03153,992,077 - 153,998,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,491,664 - 142,497,446 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13142,397,247 - 142,402,918 (+)NCBI
Celera3139,391,601 - 139,397,369 (+)NCBICelera
Cytogenetic Map3q41NCBI
TCF15
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3820604,257 - 610,309 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl20604,257 - 610,309 (-)EnsemblGRCh38hg38GRCh38
GRCh3720584,901 - 590,953 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3620532,637 - 538,910 (-)NCBINCBI36Build 36hg18NCBI36
Build 3420532,636 - 538,910NCBI
Celera20679,462 - 685,735 (-)NCBICelera
Cytogenetic Map20p13NCBI
HuRef20535,944 - 542,217 (-)NCBIHuRef
CHM1_120584,649 - 590,913 (-)NCBICHM1_1
T2T-CHM13v2.020647,994 - 654,046 (-)NCBIT2T-CHM13v2.0
Tcf15
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392151,984,973 - 151,991,017 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2151,985,481 - 151,991,017 (+)EnsemblGRCm39 Ensembl
GRCm382152,143,056 - 152,149,097 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2152,143,561 - 152,149,097 (+)EnsemblGRCm38mm10GRCm38
MGSCv372151,969,345 - 151,974,833 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362151,835,013 - 151,840,538 (+)NCBIMGSCv36mm8
Celera2157,959,706 - 157,965,194 (+)NCBICelera
Cytogenetic Map2G3NCBI
cM Map274.83NCBI
Tcf15
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955597446,855 - 451,949 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955597446,489 - 452,003 (-)NCBIChiLan1.0ChiLan1.0
TCF15
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.120581,915 - 587,644 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v020811,907 - 817,971 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TCF15
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12420,274,113 - 20,281,081 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2420,274,050 - 20,280,270 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2419,925,930 - 19,932,479 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02420,965,005 - 20,971,592 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2420,964,975 - 20,971,210 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12420,240,077 - 20,246,616 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02420,345,815 - 20,352,308 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02420,776,922 - 20,783,474 (+)NCBIUU_Cfam_GSD_1.0
TCF15
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1734,626,670 - 34,633,263 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11734,626,682 - 34,632,881 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21739,268,048 - 39,274,562 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TCF15
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1255,909,945 - 55,916,186 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl255,910,030 - 55,915,600 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660788,037,064 - 8,043,307 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tcf15
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247411,689,431 - 1,694,815 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247411,689,397 - 1,694,934 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tcf15
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:199
Count of miRNA genes:143
Interacting mature miRNAs:160
Transcripts:ENSRNOT00000000013
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3140069424146976080Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 11 2 2 2 5
Low 2 32 36 20 19 20 8 11 66 34 33 11 8
Below cutoff 1 15 15 15 8 1 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001168579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JACYVU010000119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000013   ⟹   ENSRNOP00000000013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3140,638,984 - 140,644,766 (+)Ensembl
Rnor_6.0 Ensembl3147,643,250 - 147,649,504 (+)Ensembl
RefSeq Acc Id: NM_001168579   ⟹   NP_001162051
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23140,638,984 - 140,644,766 (+)NCBI
Rnor_6.03147,643,250 - 147,649,511 (+)NCBI
Rnor_5.03153,992,077 - 153,998,338 (+)NCBI
RGSC_v3.43142,491,664 - 142,497,446 (+)RGD
Celera3139,391,601 - 139,397,369 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001162051 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001162051   ⟸   NM_001168579
- UniProtKB: D3ZEK9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000013   ⟸   ENSRNOT00000000013
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZEK9-F1-model_v2 AlphaFold D3ZEK9 1-195 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308464 AgrOrtholog
BioCyc Gene G2FUF-47280 BioCyc
Ensembl Genes ENSRNOG00000000012 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000013 ENTREZGENE
  ENSRNOP00000000013.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000013 ENTREZGENE
  ENSRNOT00000000013.6 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:296272 UniProtKB/TrEMBL
NCBI Gene 296272 ENTREZGENE
Pfam HLH UniProtKB/TrEMBL
PhenoGen Tcf15 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt D3ZEK9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tcf15  transcription factor 15   Tcf15_predicted  transcription factor 15 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tcf15_predicted  transcription factor 15 (predicted)      Symbol and Name status set to approved 70820 APPROVED